One read has many alignments starting at the same position

[seb567]

Dear SEQanswers,

I have a particular gene. I use its sequence as a reference to gather an atlas of variations induced by some enzyme, whose target is located within the said gene sequence.


The sequence of the region of interest follows.

gatattgatattggtcttaatatgacttgttttcattgtt[COLOR="Red"]ctca[/COLOR]ggtac[COLOR="Red"]ctca[/COLOR]gccagcatggcagcctctttcccacccaccttgggactca

In the sequence, two repeated 4-mers are colored in red.


I also happen to have two short reads obtained by DNA sequencing.

FORWARD:

gatattgatattggtcttaatatgacttgttttcattgttctcagccagcatggcagcctctttcccacccac


REVERSE:

tggtcttaatatgacttgttttcattgttctcagccagcatggcagcctctttcccacccaccttgggactca


Aligning these sequences onto the aforementioned reference sequence can potentially produce at least 5 alignments, regardless of utilized alignment software & algorithms.




Alignment 1

gatattgatattggtcttaatatgacttgttttcattgttctca---------gccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgttctca---------gccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgtt[COLOR="Red"]ctca[/COLOR]ggtac[COLOR="Red"]ctca[/COLOR]gccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 2

gatattgatattggtcttaatatgacttgttttcattgttctc---------agccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgttctc---------agccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgtt[COLOR="Red"]ctca[/COLOR]ggtac[COLOR="Red"]ctca[/COLOR]gccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 3

gatattgatattggtcttaatatgacttgttttcattgttct---------cagccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgttct---------cagccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgtt[COLOR="Red"]ctca[/COLOR]ggtac[COLOR="Red"]ctca[/COLOR]gccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 4

gatattgatattggtcttaatatgacttgttttcattgttc---------tcagccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgttc---------tcagccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgtt[COLOR="Red"]ctca[/COLOR]ggtac[COLOR="Red"]ctca[/COLOR]gccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 5

gatattgatattggtcttaatatgacttgttttcattgtt---------ctcagccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgtt---------ctcagccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgtt[COLOR="Red"]ctca[/COLOR]ggtac[COLOR="Red"]ctca[/COLOR]gccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 6

gatattgatattggtcttaatatgacttgttttcattgt--t-------ctcagccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgt--t-------ctcagccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgtt[COLOR="Red"]ctca[/COLOR]ggtac[COLOR="Red"]ctca[/COLOR]gccagcatggcagcctctttcccacccaccttgggactca GENE

(alignments omitted)


I can rule out the alignment number 6 and similar omitted alignments by considering them too complex in comparison to the 5 others.



Therefore, there is a deletion of 9 nucleotides.

However, the deletion can potentially start at 5 different positions.


Based solely on sequence information, I think there is just nothing that can be done to retrieve the true starting position of the deletion.



SEQanswers, what do you think ?

-Seb

[swbarnes2]

There is no "true" start. But there's probably a guideline as to whether one reports alignment 1 or 4. 4 puts the deletion as far left as possible, 1 puts it as far right as possible.

I'm not sure that current SNP databases are currently consistent about this; I'm pretty sure I found a few places in the mouse genome where the same indel was reported under two ID's because of ambiguities like that.

So if you don't know which way is preferred, pick one, and make note of which way you picked.